African Journal of
Agricultural Research

  • Abbreviation: Afr. J. Agric. Res.
  • Language: English
  • ISSN: 1991-637X
  • DOI: 10.5897/AJAR
  • Start Year: 2006
  • Published Articles: 6638

Full Length Research Paper

In silico identification of putative expressed sequence tag (EST)-simple sequence repeats (SSRs) markers of resistance to Meloidogyne spp. in common bean

Lucas Donizetti Vieira
  • Lucas Donizetti Vieira
  • Department of Genetics and Molecular Biology, Universidade Federal de Goiás, Goiânia, Brazil.
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Juliana Oliveira da Silva
  • Juliana Oliveira da Silva
  • Department of Agronomy, IF Goiano, Urutaí, Goiás, Brazil.
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Caio César de Oliveira Pereira
  • Caio César de Oliveira Pereira
  • Department of Agronomy, IF Goiano, Urutaí, Goiás, Brazil.
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Solange Aline de Carvalho
  • Solange Aline de Carvalho
  • Department of Biology, IF Goiano, Urutaí, Goiás, Brazil.
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Ricardo Diogenes Dias Silveira
  • Ricardo Diogenes Dias Silveira
  • Department of Biology, IF Goiano, Urutaí, Goiás, Brazil.
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Guilherme Malafaia
  • Guilherme Malafaia
  • Department of Biology, IF Goiano, Urutaí, Goiás, Brazil.
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Ivandilson Pessoa Pinto de Menezes
  • Ivandilson Pessoa Pinto de Menezes
  • Department of Biology, IF Goiano, Urutaí, Goiás, Brazil.
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  •  Received: 10 April 2016
  •  Accepted: 16 May 2016
  •  Published: 09 June 2016

Abstract

Expressed sequences are important sources in the development of functional heterologous microsatellite markers in phylogenetic related groups, that is, soybean and commom bean. The objective of this work was to identify and characterize expressed sequence tag (EST)-simple sequence repeats (SSRs) in silico candidates of resistance to Meloidogyne spp. in common bean. Seven DNA sequences from soybean associated with genetic resistance have been identified and obtained in the NCBI database. Its homology in common bean genome was verified using the BLAST tool. The cellular processes involved were also checked using the Blast2GO program. The identification of microsatellite markers and design of the primer pairs was performed using the SSRLocator and Primer3 programs, respectively. The transferability rate of common beans the target sequences identified was 86%, demonstrating the power of success of this method. All the cellular processes involved in the original DNA sequences were verified from EST on beans, with E-value between 0 and 2.9×10-168. Fifteen EST-SSRs candidates for common bean resistance were identified, which have proved to be suitable for their amplification by PCR. The transferability analysis of ESTs related to resistance to Meloidogyne spp., especially among soybeans and common beans is efficient. Based on this study, 15 EST-SSRs candidates are available for validation and later use.

Key words: simple sequence repeats (SSRs) markers, assisted selection, ontology, pre-breeding.